In Alegria watershed, an important alluvial aquifer presents a significant rule within the agricultural contamination (including nitrates and pesticides). Pollutants are transported from the soil to the river through this alluvial aquifer or directly by runoff during flood events. This study – included in the AguaFlash (http://www.aguaflash-sudoe.eu/) European project – aims to understand contaminant load dynamics and the contribution of the alluvial aquifer and runoff to river contamination. The SWAT model (2009 version) has been applied from October 2009 to March 2011 in Alegria agricultural watershed located in Basque Country. The alluvial aquifer represents 50% of the watershed and is located in a vulnerable zone to nitrates pollution. Water quality measurements at daily time-step have been used to assess fluxes and nitrates, suspended sediments and pesticides transport. During low flow and flood events, simulated concentrations have been compared to data collected at the watershed outlet.